Thank Frank for the summary on an interesting topic. Forgot to attach papers last time. Here are a couple of experimental examples of enhancing the crystallisation under Dr. Derewenda’ surface entropy reduction theory, which were published in 2009. >From difficult to be crystallised, to obtain crystals after surface flexible >residues mutation, leading to oligomerisation in crystal packing...... >Thought the preference of the oligmeric ensemble could be a type of surface >entropy reduction to get explained. 1)https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2659884/ 2)https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2739605/
A quote from the above second paper “Importantly, three out of four YphP molecules in the asymmetric unit form crystal contacts directly via the low-entropy patches generated by the Q100A, E101A substitutions. This pattern suggests that an oligomeric ensemble might first form transiently in solution and then be incorporated into the crystal via surface patches introduced by mutagenesis. A similar mechanism is observed for other proteins crystallized by this approach (Z. S. Derewenda, unpublished).” Minmin On Wednesday, December 1, 2021, 7:33 am, Frank von Delft <frank.vonde...@cmd.ox.ac.uk> wrote: Dear all, thanks all for the several references you emailed around. Here's a summary: A Suite of Engineered GFP Molecules for Oligomeric Scaffolding https://www.sciencedirect.com/science/article/pii/S0969212615002890 Dimerization properties of the RpBphP2 chromophore-binding domain crystallized by homologue-directed mutagenesis https://pubmed.ncbi.nlm.nih.gov/22868772/ An approach to crystallizing proteins by synthetic symmetrization https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1637565/ Why protein crystals favour some space-groups over others https://www.nature.com/articles/nsb1295-1062 Infinite Assembly of Folded Proteins in Evolution, Disease,and Engineering https://onlinelibrary.wiley.com/doi/pdf/10.1002/anie.201806092 James Holton duly challenged me, and here's my reply: JH: If I told you "no, that's not true", how would you go about proving me wrong? What would that data look like? -- FvD: Geezus, I don't know! It's not me that hurled this brainfart around the grant funding agencies 20 years ago... That's why I asked the Social Brain. But my primary goal was to have something to stick into the introduction to a paper, so that has been achieved. Whether it's ethical to perpetuate a brainfart by citing other expressions of the brainfart is a reasonable question, but this one would rank quite low on the impact-of-transgression scale, methinks. But Dhiraj's reply to my original question is a surely a better one: "Recently there were few articles where synthetic symmetrization was used to enhance the crystallizability. proteins used were MBP, lysozyme and GFP to name a few." It implies the weight-of-evidence is out there - hint to you enterprising students, looking for something *actually useful* to write a review about! Frank On 12/11/2021 14:52, Frank von Delft wrote: Hello all Two decades ago, I remember (!) much talk about a reason that bacterial proteins crystallize "more easily" is that they tend to come as oligomers (dimers and up), and that this internal symmetry made them happier to crystallize. Did anybody ever publish hard evidence? Or even, is there a primary citation for the idea? Thanks Frank ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
